Additional file 6 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 6. Supplementary Table 6. Top GO Biological Processes, GO Cellular Components, GO Molecular Functions, Reactome, and KEGG Pathways enriched from significantly differentially methylated regions (FDR 0.075) identified when overlapping DMRs identified in the main analysis with DMRs identified when samples were limited to participants aged 50 and above at recruitment

Additional file 7 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 7: Fig. S2. Relative proportions of hypermethylated, hypomethylated and all regions of the dataset when annotated by Enhancer status as annotated in the FANTOM5 enhancer atlas for the GM12878 human lymphoblastoid cell line; andgenic annotations

Additional file 10 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 10: Fig. S3. ROC curves for the tested classifiers. Individual ROC curves are shown for each cross-validation fold. SVM: support vector machines; PLR: penalized logistic regression; NNET: neural network; RF: random forests; LogitBoost: boosted logistic regressison; KNN: k-nearest neighbours; PAM: Prediction Analysis for Microarrays; RPART: classification and regression tre

Additional file 8 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 8. Supplementary Table 7. Genomic regions in which DNA methylation is significantly correlated to length of time to diagnosis (days) by Kendall rank correlation (FDR < 0.05)

Additional file 1 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 1. Supplementary Methods, Supplementary Tables and References

Additional file 2 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 2: Fig. S1. Distribution of participants within the model development and held-out sample sets byage at recruitment,body mass index,exit age, and proportion-of-whole graphs illustrating the distribution of participants bytumour subtype,menopausal status at recruitment,hormonal contraceptive use,hormone therapy use, andpregnancy history

Additional file 9 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 9. Supplementary Table 9. Genomic regions utilized by the PAM prediction model

Additional file 4 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 4. Supplementary Table 4. List of significantly differentially methylated regions (FDR 0.075) between cases and matched controls in prospectively-collected buffy-coat samples, limited to samples collected from women diagnosed after the age of 50

Additional file 5 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 5. Supplementary Table 5. Top GO Biological Processes, GO Cellular Components, GO Molecular Functions, Reactome, and KEGG Pathways enriched from significantly differentially methylated regions (FDR 0.075) identified when comparing between cases and matched controls in prospectively-collected buffy-coat samples

Additional file 3 of Buffy coat signatures of breast cancer risk in a prospective cohort study

Additional file 3. Supplementary Table 3. List of significantly differentially methylated regions (FDR 0.075) between cases and matched controls in prospectively-collected buffy-coat samples. The correlation between DNA methylation levels at these regions to time to diagnosis was determined by Kendall rank correlation